The East Asian wild apples, Malus baccata (L.) Borkh and Malus hupehensis (Pamp.) Rehder., are additional contributors to the genomes of cultivated European and Chinese varieties

The domestication process in long-lived plant perennials differs dramatically from that of annuals, with a huge amount of genetic exchange between crop and wild populations. Though apple is a major fruit crop grown worldwide, the contribution of wild apple species to the genetic makeup of the cultivated apple genome remains a topic of intense study. We used population genomics approaches to investigate the contributions of several wild apple species to European and Chinese rootstock and dessert genomes, with a focus on the extent of wild-crop gene flow. Population genetic structure inferences revealed that the East Asian wild apples, Malus baccata (L.) Borkh and M. hupehensis (Pamp.), form a single panmictic group, and that the European dessert and rootstock apples form a specific gene pool whereas the Chinese dessert and rootstock apples were a mixture of three wild gene pools, suggesting different evolutionary histories of European and Chinese apple varieties. Coalescent-based inferences and gene flow estimates indicated that M. baccata - M. hupehensis contributed to the genome of both European and Chinese cultivated apples through wild-to-crop introgressions, and not as an initial contributor as previously supposed. We also confirmed the contribution through wild-to-crop introgressions of Malus sylvestris Mill. to the cultivated apple genome. Apple tree domestication is therefore one example in woody perennials that involved gene flow from several wild species from multiple geographical areas. This study provides an example of a complex protracted process of domestication in long-lived plant perennials, and is a starting point for apple breeding programmes.

Ecological and evolutionary drivers of phenotypic and genetic variation in the European crabapple (Malus sylvestris (L.) Mill.), a wild relative of the cultivated apple

BACKGROUND AND AIMS

Studying the relationship between phenotypic and genetic variation in populations distributed across environmental gradients can help us understand the ecological and evolutionary processes involved in population divergence. We investigated the patterns of genetic and phenotypic diversity in the European crabapple, Malus sylvestris, a wild relative of the cultivated apple (Malus domestica) that occurs naturally across Europe in areas subjected to different climate conditions, to test for divergence among populations.

METHODS

Growth rates and traits related to carbon uptake in seedlings collected across Europe were measured under controlled conditions and associated with the genetic status of the seedlings, which was assessed using 13 microsatellite loci and Bayesian clustering method. Isolation-by-distance, -by-climate, and -by-adaptation patterns, which can explain genetic and phenotypic differentiation among M. sylvestris populations, were also tested.

KEY RESULTS

A total of 11.6% of seedlings were introgressed by M. domestica, indicating that crop-wild gene flow is ongoing in Europe. The remaining seedlings (88.4%) belonged to seven M. sylvestris populations. Significant phenotypic trait variation among M. sylvestris populations was observed. We did not observe significant isolation-by-adaptation; however, the significant association between genetic variation and the climate during the last glacial maximum suggests that there has been local adaptation of M. sylvestris to past climates.

CONCLUSIONS

This study provides insight into the phenotypic and genetic differentiation among populations of a wild relative of the cultivated apple. This may help us better utilize its diversity and provide options for mitigating the impact of climate change on the cultivated apple through breeding.

Crop domestication as a step towards reproductive isolation

Speciation, Darwin's mystery of mysteries, is a continuous process that results in genomic divergence accompanied by the gradual increment of reproductive barriers between lineages. Since the beginning of research on the genetics of speciation, several questions have emerged such as: What are the genetic bases of incompatibilities? How many loci are necessary to prevent hybridization and how are they distributed along genomes? Can speciation occur despite gene flow and how common is ecological speciation? Early stages of divergence are key to understand the ecology and genetics of speciation, and semi-isolated species where hybrids can still be produced are particularly relevant This article is protected by copyright. All rights reserved.

Evidence of an additional centre of apple domestication in Iran, with contributions from the Caucasian crab apple Malus orientalis Uglitzk. to the cultivated apple gene pool

Divergence processes in crop-wild fruit tree complexes in pivotal regions for plant domestication such as the Caucasus and Iran remain little studied. We investigated anthropogenic and natural divergence processes in apples in these regions using 26 microsatellite markers amplified in 550 wild and cultivated samples. We found two genetically distinct cultivated populations in Iran that are differentiated from Malus domestica, the standard cultivated apple worldwide. Coalescent-based inferences showed that these two cultivated populations originated from specific domestication events of Malus orientalis in Iran. We found evidence of substantial wild-crop and crop-crop gene flow in the Caucasus and Iran, as has been described in apple in Europe. In addition, we identified seven genetically differentiated populations of wild apple (M. orientalis), not introgressed by the cultivated apple. Niche modelling combined with genetic diversity estimates indicated that these wild populations likely resulted from range changes during past glaciations. This study identifies Iran as a key region in the domestication of apple and M. orientalis as an additional contributor to the cultivated apple gene pool. Domestication of the apple tree therefore involved multiple origins of domestication in different geographic locations and substantial crop-wild hybridization, as found in other fruit trees. This study also highlights the impact of climate change on the natural divergence of a wild fruit tree and provides a starting point for apple conservation and breeding programmes in the Caucasus and Iran.

The relative role of plasticity and demographic history in Capsella bursa-pastoris: a common garden experiment in Asia and Europe

The colonization success of a species depends on the interplay between its phenotypic plasticity, adaptive potential and demographic history. Assessing their relative contributions during the different phases of a species range expansion is challenging, and requires large-scale experiments. Here, we investigated the relative contributions of plasticity, performance and demographic history to the worldwide expansion of the shepherd's purse, Capsella bursa-pastoris. We installed two large common gardens of the shepherd's purse, a young, self-fertilizing, allopolyploid weed with a worldwide distribution. One common garden was located in Europe, the other in Asia. We used accessions from three distinct genetic clusters (Middle East, Europe and Asia) that reflect the demographic history of the species. Several life-history traits were measured. To explain the phenotypic variation between and within genetic clusters, we analysed the effects of (i) the genetic clusters, (ii) the phenotypic plasticity and its association to fitness and (iii) the distance in terms of bioclimatic variables between the sampling site of an accession and the common garden, i.e. the environmental distance. Our experiment showed that (i) the performance of C. bursa-pastoris is closely related to its high phenotypic plasticity; (ii) within a common garden, genetic cluster was a main determinant of phenotypic differences; and (iii) at the scale of the experiment, the effect of environmental distance to the common garden could not be distinguished from that of genetic clusters. Phenotypic plasticity and demographic history both play important role at different stages of range expansion. The success of the worldwide expansion of C. bursa-pastoris was undoubtedly influenced by its strong phenotypic plasticity.

Evolutionary Genetics of Crop-Wild Complexes

Since Darwin's time, the role of crop wild relatives (CWR), landraces, and cultivated genepools in shaping plant diversity and boosting food resources has been a major question [...].

Induced mutations in SlE8 and SlACO1 control tomato fruit maturation and shelf-life

Fruit maturation and softening are critical traits that control fruit shelf-life. In the climacteric tomato (Solanum lycopersicum L.) fruit, ethylene plays a key role in fruit ripening and softening. We characterized two related proteins with contrasting impact on ethylene production, ACC oxidase 1 (SlACO1) and SlE8. We found SlACO1 and SlE8 to be highly expressed during fruit ripening. To identify loss-of-function alleles, we analysed the tomato genetic diversity but we did not find any natural mutations impairing the function of these proteins. We also found the two loci evolving under purifying selection. To engineer hypomorphic alleles, we used TILLING (target-induced local lesions in genomes) to screen a tomato ethylmethane sulfonate-mutagenized population. We found 13 mutants that we phenotyped for ethylene production, shelf-life, firmness, conductivity, and soluble solid content in tomato fruits. The data demonstrated that slaco1-1 and slaco1-2 alleles could be used to improve fruit shelf-life, and that sle8-1 and sle8-2 alleles could be used to accelerate ripening. This study highlights further the importance of SlACO1 and SlE8 in ethylene production in tomato fruit and how they might be used for post-harvest fruit preservation or speeding up fruit maturation.

Study of the genetic and phenotypic variation among wild and cultivated clary sages provides interesting avenues for breeding programs of a perfume, medicinal and aromatic plant

A road-map of the genetic and phenotypic diversities in both crops and their wild related species can help identifying valuable genetic resources for further crop breeding. The clary sage (Salvia sclarea L.), a perfume, medicinal and aromatic plant, is used for sclareol production and ornamental purposes. Despite its wide use in the field of cosmetics, the phenotypic and genetic diversity of wild and cultivated clary sages remains to be explored. We characterized the genetic and phenotypic variation of a collection of six wild S. sclarea populations from Croatia, sampled along an altitudinal gradient, and, of populations of three S. sclarea cultivars. We showed low level of genetic diversity for the two S. sclarea traditional cultivars used for essential oil production and for ornamental purposes, respectively. In contrast, a recent cultivar resulting from new breeding methods, which involve hybridizations among several genotypes rather than traditional recurrent selection and self-crosses over time, showed high genetic diversity. We also observed a marked phenotypic differentiation for the ornamental clary sage compared with other cultivated and wild clary sages. Instead, the two cultivars used for essential oil production, a traditional and a recent one, respectively, were not phenotypically differentiated from the wild Croatian populations. Our results also featured some wild populations with high sclareol content and early-flowering phenotypes as good candidates for future breeding programs. This study opens up perspectives for basic research aiming at understanding the impact of breeding methods on clary sage evolution, and highlights interesting avenues for clary breeding programs.

Population genomics of apricots unravels domestication history and adaptive events

Among crop fruit trees, the apricot (Prunus armeniaca) provides an excellent model to study divergence and adaptation processes. Here, we obtain nearly 600 Armeniaca apricot genomes and four high-quality assemblies anchored on genetic maps. Chinese and European apricots form two differentiated gene pools with high genetic diversity, resulting from independent domestication events from distinct wild Central Asian populations, and with subsequent gene flow. A relatively low proportion of the genome is affected by selection. Different genomic regions show footprints of selection in European and Chinese cultivated apricots, despite convergent phenotypic traits, with predicted functions in both groups involved in the perennial life cycle, fruit quality and disease resistance. Selection footprints appear more abundant in European apricots, with a hotspot on chromosome 4, while admixture is more pervasive in Chinese cultivated apricots. Our study provides clues to the biology of selected traits and targets for fruit tree research and breeding.

Novel genomic approaches to study antagonistic coevolution between hosts and parasites

Host-parasite coevolution is ubiquitous, shaping genetic and phenotypic diversity and the evolutionary trajectory of interacting species. With the advances of high throughput sequencing technologies applicable to model and non-model organisms alike, it is now feasible to study in greater detail (a) the genetic underpinnings of coevolution, (b) the speed and type of dynamics at coevolving loci, and (c) the genomic consequences of coevolution. This review focuses on three recently developed approaches that leverage information from host and parasite full genome data simultaneously to pinpoint coevolving loci and draw inference on the coevolutionary history. First, co-genome-wide association study (co-GWAS) methods allow pinpointing the loci underlying host-parasite interactions. These methods focus on detecting associations between genetic variants and the outcome of experimental infection tests or on correlations between genomes of naturally infected hosts and their infecting parasites. Second, extensions to population genomics methods can detect genes under coevolution and infer the coevolutionary history, such as fitness costs. Third, correlations between host and parasite population size in time are indicative of coevolution, and polymorphism levels across independent spatially distributed populations of hosts and parasites can reveal coevolutionary loci and infer coevolutionary history. We describe the principles of these three approaches and discuss their advantages and limitations based on coevolutionary theory. We present recommendations for their application to various host (prokaryotes, fungi, plants, and animals) and parasite (viruses, bacteria, fungi, and macroparasites) species. We conclude by pointing out methodological and theoretical gaps to be filled to extract maximum information from full genome data and thereby to shed light on the molecular underpinnings of coevolution.

Early evolution of reproductive isolation: A case of weak inbreeder/strong outbreeder leads to an intraspecific hybridization barrier in Arabidopsis lyrata

Reproductive strategies play a major role in plant speciation. Notably, transitions from outcrossing to selfing may lead to relaxed sexual selection and parental conflict. Shifts in mating systems can affect maternal and paternal interests, and thus parent-specific influence on endosperm development, leading to reproductive isolation: if selfing and outcrossing species hybridize, the resulting seeds may not be viable due to endosperm failure. Nevertheless, it remains unclear how the switch in mating systems can impact reproductive isolation between recently diverged lineages, that is, during the process of speciation. We investigated this question using Arabidopsis lyrata, which recently transitioned to selfing (10,000 years ago) in certain North American populations, where European populations remain outcrossing. We performed reciprocal crosses between selfers and outcrossers, and measured seed viability and endosperm development. We show that parental genomes in the hybrid seed negatively interact, as predicted by parental conflict. This leads to extensive hybrid seed lethality associated with endosperm cellularization disturbance. Our results suggest that this is primarily driven by divergent evolution of the paternal genome between selfers and outcrossers. In addition, we observed other hybrid seed defects, suggesting that sex-specific interests are not the only processes contributing to postzygotic reproductive isolation.

The complex evolutionary history of apricots: Species divergence, gene flow and multiple domestication events

Domestication is an excellent model to study diversification and this evolutionary process can be different in perennial plants, such as fruit trees, compared to annual crops. Here, we inferred the history of wild apricot species divergence and of apricot domestication history across Eurasia, with a special focus on Central and Eastern Asia, based on microsatellite markers and approximate Bayesian computation. We significantly extended our previous sampling of apricots in Europe and Central Asia towards Eastern Asia, resulting in a total sample of 271 cultivated samples and 306 wild apricots across Eurasia, mainly Prunus armeniaca and Prunus sibirica, with some Prunus mume and Prunus mandshurica. We recovered wild Chinese species as genetically differentiated clusters, with P. sibirica being divided into two clusters, one possibly resulting from hybridization with P. armeniaca. Central Asia also appeared as a diversification centre of wild apricots. We further revealed at least three domestication events, without bottlenecks, that gave rise to European, Southern Central Asian and Chinese cultivated apricots, with ancient gene flow among them. The domestication event in China possibly resulted from ancient hybridization between wild populations from Central and Eastern Asia. We also detected extensive footprints of recent admixture in all groups of cultivated apricots. Our results thus show that apricot is an excellent model for studying speciation and domestication in long-lived perennial fruit trees.

Understanding Adaptation, Coevolution, Host Specialization, and Mating System in Castrating Anther-Smut Fungi by Combining Population and Comparative Genomics

Anther-smut fungi provide a powerful system to study host-pathogen specialization and coevolution, with hundreds of Microbotryum species specialized on diverse Caryophyllaceae plants, castrating their hosts through manipulation of the hosts' reproductive organs to facilitate disease transmission. Microbotryum fungi have exceptional genomic characteristics, including dimorphic mating-type chromosomes, that make this genus anexcellent model for studying the evolution of mating systems and their influence on population genetics structure and adaptive potential. Important insights into adaptation, coevolution, host specialization, and mating system evolution have been gained using anther-smut fungi, with new insights made possible by the recent advent of genomic approaches. We illustrate with Microbotryum case studies how using a combination of comparative genomics, population genomics, and transcriptomics approaches enables the integration of different evolutionary perspectives across different timescales. We also highlight current challenges and suggest future studies that will contribute to advancing our understanding of the mechanisms underlying adaptive processes in populations of fungal pathogens.

A Multifaceted Overview of Apple Tree Domestication

The apple is an iconic tree and a major fruit crop worldwide. It is also a model species for the study of the evolutionary processes and genomic basis underlying the domestication of clonally propagated perennial crops. Multidisciplinary approaches from across Eurasia have documented the pace and process of cultivation of this remarkable crop. While population genetics and genomics have revealed the overall domestication history of apple across Eurasia, untangling the evolutionary processes involved, archeobotany has helped to document the transition from gathering and using apples to the practice of cultivation. Further studies integrating archeogenetic and archeogenomic approaches will bring new insights about key traits involved in apple domestication. Such knowledge has potential to boost innovation in present-day apple breeding.

Apple whole genome sequences: recent advances and new prospects

In 2010, a major scientific milestone was achieved for tree fruit crops: publication of the first draft whole genome sequence (WGS) for apple (Malus domestica). This WGS, v1.0, was valuable as the initial reference for sequence information, fine mapping, gene discovery, variant discovery, and tool development. A new, high quality apple WGS, GDDH13 v1.1, was released in 2017 and now serves as the reference genome for apple. Over the past decade, these apple WGSs have had an enormous impact on our understanding of apple biological functioning, trait physiology and inheritance, leading to practical applications for improving this highly valued crop. Causal gene identities for phenotypes of fundamental and practical interest can today be discovered much more rapidly. Genome-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and pedigrees. High-density genetic maps are constructed efficiently and quantitative trait loci for valuable traits are readily associated with positional candidate genes and/or converted into diagnostic tests for breeders. We understand the species, geographical, and genomic origins of domesticated apple more precisely, as well as its relationship to wild relatives. The WGS has turbo-charged application of these classical research steps to crop improvement and drives innovative methods to achieve more durable, environmentally sound, productive, and consumer-desirable apple production. This review includes examples of basic and practical breakthroughs and challenges in using the apple WGSs. Recommendations for "what's next" focus on necessary upgrades to the genome sequence data pool, as well as for use of the data, to reach new frontiers in genomics-based scientific understanding of apple.

Paternally expressed imprinted genes associate with hybridization barriers in Capsella

Hybrid seed lethality is a widespread type of reproductive barrier among angiosperm taxa^1,2 that contributes to species divergence by preventing gene flow between natural populations^3,4. Besides its ecological importance, it is an important obstacle to plant breeding strategies ⁵ . Hybrid seed lethality is mostly due to a failure of the nourishing endosperm tissue, resulting in embryo arrest^3,6,7. The cause of this failure is a parental dosage imbalance in the endosperm that can be a consequence of either differences in parental ploidy levels or differences in the 'effective ploidy', also known as the endosperm balance number (EBN)^8,9. Hybrid seed defects exhibit a parent-of-origin pattern^3,6,7, suggesting that differences in number or expression strength of parent-of-origin-specific imprinted genes underpin, as the primary or the secondary cause, the molecular basis of the EBN^7,10. Here, we have tested this concept in the genus Capsella and show that the effective ploidy of three Capsella species correlates with the number and expression level of paternally expressed genes (PEGs). Importantly, the number of PEGs and the effective ploidy decrease with the selfing history of a species: the obligate outbreeder Capsella grandiflora had the highest effective ploidy, followed by the recent selfer Capsella rubella and the ancient selfer Capsella orientalis. PEGs were associated with the presence of transposable elements and their silencing mark, DNA methylation in CHH context (where H denotes any base except C). This suggests that transposable elements have driven the imprintome divergence between Capsella species. Together, we propose that variation in transposable element insertions, the resulting differences in PEG number and divergence in their expression level form one component of the effective ploidy variation between species of different breeding system histories, and, as a consequence, allow the establishment of endosperm-based hybridization barriers.

On the origins and domestication of the olive: a review and perspectives

Background

Unravelling domestication processes is crucial for understanding how species respond to anthropogenic pressures, forecasting crop responses to future global changes and improving breeding programmes. Domestication processes for clonally propagated perennials differ markedly from those for seed-propagated annual crops, mostly due to long generation times, clonal propagation and recurrent admixture with local forms, leading to a limited number of generations of selection from wild ancestors. However, additional case studies are required to document this process more fully.

Scope

The olive is an iconic species in Mediterranean cultural history. Its multiple uses and omnipresence in traditional agrosystems have made this species an economic pillar and cornerstone of Mediterranean agriculture. However, major questions about the domestication history of the olive remain unanswered. New paleobotanical, archeological, historical and molecular data have recently accumulated for olive, making it timely to carry out a critical re-evaluation of the biogeography of wild olives and the history of their cultivation. We review here the chronological history of wild olives and discuss the questions that remain unanswered, or even unasked, about their domestication history in the Mediterranean Basin. We argue that more detailed ecological genomics studies of wild and cultivated olives are crucial to improve our understanding of olive domestication. Multidisciplinary research integrating genomics, metagenomics and community ecology will make it possible to decipher the evolutionary ecology of one of the most iconic domesticated fruit trees worldwide.

Conclusion

The olive is a relevant model for improving our knowledge of domestication processes in clonally propagated perennial crops, particularly those of the Mediterranean Basin. Future studies on the ecological and genomic shifts linked to domestication in olive and its associated community will provide insight into the phenotypic and molecular bases of crop adaptation to human uses.

Co-occurrence and hybridization of anther-smut pathogens specialized on Dianthus hosts

Host specialization has important consequences for the diversification and ecological interactions of obligate pathogens. The anther-smut disease of natural plant populations, caused by Microbotryum fungi, has been characterized by specialized host-pathogen interactions, which contribute in part to the isolation among these numerous fungal species. This study investigated the molecular variation of Microbotryum pathogens within the geographic and host-specific distributions on wild Dianthus species in southern European Alps. In contrast to prior studies on this pathogen genus, a range of overlapping host specificities was observed for four delineated Microbotryum lineages on Dianthus hosts, and their frequent co-occurrence within single-host populations was quantified at local and regional scales. In addition to potential consequences for direct pathogen competition, the sympatry of Microbotryum lineages led to hybridization between them in many populations, and these admixed genotypes suffered significant meiotic sterility. Therefore, this investigation of the anther-smut fungi reveals how variation in the degrees of host specificity can have major implications for ecological interactions and genetic integrity of differentiated pathogen lineages.

Crop-to-wild gene flow and its fitness consequences for a wild fruit tree: Towards a comprehensive conservation strategy of the wild apple in Europe

Crop-to-wild gene flow can reduce the fitness and genetic integrity of wild species. Malus sylvestris, the European crab-apple fruit tree in particular, is threatened by the disappearance of its habitat and by gene flow from its domesticated relative, Malus domestica. With the aims of evaluating threats for M. sylvestris and of formulating recommendations for its conservation, we studied here, using microsatellite markers and growth experiments: (i) hybridization rates in seeds and trees from a French forest and in seeds used for replanting crab apples in agrosystems and in forests, (ii) the impact of the level of M. domestica ancestry on individual tree fitness and (iii) pollen dispersal abilities in relation to crop-to-wild gene flow. We found substantial contemporary crop-to-wild gene flow in crab-apple tree populations and superior fitness of hybrids compared to wild seeds and seedlings. Using paternity analyses, we showed that pollen dispersal could occur up to 4 km and decreased with tree density. The seed network furnishing the wild apple reintroduction agroforestry programmes was found to suffer from poor genetic diversity, introgressions and species misidentification. Overall, our findings indicate supported threats for the European wild apple steering us to provide precise recommendations for its conservation.

Strong phylogeographic co-structure between the anther-smut fungus and its white campion host

Although congruence between host and pathogen phylogenies has been extensively investigated, the congruence between host and pathogen genetic structures at the within-species level has received little attention. Using an unprecedented and comprehensive collection of associated plant-pathogen samples, we investigated the degree of congruence between the genetic structures across Europe of two evolutionary and ecological model organisms, the anther-smut pathogen Microbotryum lychnidis-dioicae and its host plant Silene latifolia. We demonstrated a significant and particularly strong level of host-pathogen co-structure, with three main genetic clusters displaying highly similar spatial ranges in Western Europe, Eastern Europe and Italy, respectively. Correcting for the geographical component of genetic variation, significant correlations were still found between the genetic distances of anther-smut and host populations. Inoculation experiments suggested plant local adaptation, at the cluster level, for resistance to pathogens. These findings indicate that the pathogen remained isolated in the same fragmented southern refugia as its host plant during the last glaciation, and that little long-distance dispersal has occurred since the recolonization of Europe for either the plant or the pathogen, despite their known ability to travel across continents. This, together with the inoculation results, suggests that coevolutionary and competitive processes may be drivers of host-pathogen co-structure.

New insights into the history of domesticated and wild apricots and its contribution to Plum pox virus resistance

Studying domesticated species and their wild relatives allows understanding of the mechanisms of population divergence and adaptation, and identifying valuable genetic resources. Apricot is an important fruit in the Northern hemisphere, where it is threatened by the Plum pox virus (PPV), causing the sharka disease. The histories of apricot domestication and of its resistance to sharka are however still poorly understood. We used 18 microsatellite markers to genotype a collection of 230 wild trees from Central Asia and 142 cultivated apricots as representatives of the worldwide cultivated apricot germplasm; we also performed experimental PPV inoculation tests. The genetic markers revealed highest levels of diversity in Central Asian and Chinese wild and cultivated apricots, confirming an origin in this region. In cultivated apricots, Chinese accessions were differentiated from more Western accessions, while cultivated apricots were differentiated from wild apricots. An approximate Bayesian approach indicated that apricots likely underwent two independent domestication events, with bottlenecks, from the same wild population. Central Asian native apricots exhibited genetic subdivision and high frequency of resistance to sharka. Altogether, our results contribute to the understanding of the domestication history of cultivated apricot and point to valuable genetic diversity in the extant genetic resources of wild apricots.

Genomic signature of successful colonization of Eurasia by the allopolyploid shepherd's purse (Capsella bursa-pastoris)

Polyploidization is a dominant feature of flowering plant evolution. However, detailed genomic analyses of the interpopulation diversification of polyploids following genome duplication are still in their infancy, mainly because of methodological limits, both in terms of sequencing and computational analyses. The shepherd's purse (Capsella bursa-pastoris) is one of the most common weed species in the world. It is highly self-fertilizing, and recent genomic data indicate that it is an allopolyploid, resulting from hybridization between the ancestors of the diploid species Capsella grandiflora and Capsella orientalis. Here, we investigated the genomic diversity of C. bursa-pastoris, its population structure and demographic history, following allopolyploidization in Eurasia. To that end, we genotyped 261 C. bursa-pastoris accessions spread across Europe, the Middle East and Asia, using genotyping-by-sequencing, leading to a total of 4274 SNPs after quality control. Bayesian clustering analyses revealed three distinct genetic clusters in Eurasia: one cluster grouping samples from Western Europe and Southeastern Siberia, the second one centred on Eastern Asia and the third one in the Middle East. Approximate Bayesian computation (ABC) supported the hypothesis that C. bursa-pastoris underwent a typical colonization history involving low gene flow among colonizing populations, likely starting from the Middle East towards Europe and followed by successive human-mediated expansions into Eastern Asia. Altogether, these findings bring new insights into the recent multistage colonization history of the allotetraploid C. bursa-pastoris and highlight ABC and genotyping-by-sequencing data as promising but still challenging tools to infer demographic histories of selfing allopolyploids.

A microRNA allele that emerged prior to apple domestication may underlie fruit size evolution

The molecular genetic mechanisms underlying fruit size remain poorly understood in perennial crops, despite size being an important agronomic trait. Here we show that the expression level of a microRNA gene (miRNA172) influences fruit size in apple. A transposon insertional allele of miRNA172 showing reduced expression associates with large fruit in an apple breeding population, whereas over-expression of miRNA172 in transgenic apple significantly reduces fruit size. The transposon insertional allele was found to be co-located with a major fruit size quantitative trait locus, fixed in cultivated apples and their wild progenitor species with relatively large fruit. This finding supports the view that the selection for large size in apple fruit was initiated prior to apple domestication, likely by large mammals, before being subsequently strengthened by humans, and also helps to explain why signatures of genetic bottlenecks and selective sweeps are normally weaker in perennial crops than in annual crops.

Genomic basis of the differences between cider and dessert apple varieties

Unraveling the genomic processes at play during variety diversification is of fundamental interest for understanding evolution, but also of applied interest in crop science. It can indeed provide knowledge on the genetic bases of traits for crop improvement and germplasm diversity management. Apple is one of the most important fruit crops in temperate regions, having both great economic and cultural values. Sweet dessert apples are used for direct consumption, while bitter cider apples are used to produce cider. Several important traits are known to differentiate the two variety types, in particular fruit size, biennial versus annual fruit bearing, and bitterness, caused by a higher content in polyphenols. Here, we used an Illumina 8k SNP chip on two core collections, of 48 dessert and 48 cider apples, respectively, for identifying genomic regions responsible for the differences between cider and dessert apples. The genome-wide level of genetic differentiation between cider and dessert apples was low, although 17 candidate regions showed signatures of divergent selection, displaying either outlier F_ST values or significant association with phenotypic traits (bitter versus sweet fruits). These candidate regions encompassed 420 genes involved in a variety of functions and metabolic pathways, including several colocalizations with QTLs for polyphenol compounds.

Hyperthermic intraperitoneal chemotherapy leads to an anticancer immune response via exposure of cell surface heat shock protein 90

The occurrence of peritoneal carcinomatosis is a major cause of treatment failure in colorectal cancer and is considered incurable. However, new therapeutic approaches have been proposed, including cytoreductive surgery combined with hyperthermic intraperitoneal chemotherapy (HIPEC). Although HIPEC has been effective in selected patients, it is not known how HIPEC prolongs a patient's lifespan. Here, we have demonstrated that HIPEC-treated tumor cells induce the activation of tumor-specific T cells and lead to vaccination against tumor cells in mice. We have established that this effect results from the HIPEC-mediated exposure of heat shock protein (HSP) 90 at the plasma membrane. Inhibition or blocking of HSP90, but not HSP70, prevented the HIPEC-mediated antitumoral vaccination. Our work raises the possibility that the HIPEC procedure not only kills tumor cells but also induces an efficient anticancer immune response, therefore opening new opportunities for cancer treatment.

Anthropogenic and natural drivers of gene flow in a temperate wild fruit tree: a basis for conservation and breeding programs in apples

Gene flow is an essential component of population adaptation and species evolution. Understanding of the natural and anthropogenic factors affecting gene flow is also critical for the development of appropriate management, breeding, and conservation programs. Here, we explored the natural and anthropogenic factors impacting crop-to-wild and within wild gene flow in apples in Europe using an unprecedented dense sampling of 1889 wild apple (Malus sylvestris) from European forests and 339 apple cultivars (Malus domestica). We made use of genetic, environmental, and ecological data (microsatellite markers, apple production across landscapes and records of apple flower visitors, respectively). We provide the first evidence that both human activities, through apple production, and human disturbance, through modifications of apple flower visitor diversity, have had a significant impact on crop-to-wild interspecific introgression rates. Our analysis also revealed the impact of previous natural climate change on historical gene flow in the nonintrogressed wild apple M. sylvestris, by identifying five distinct genetic groups in Europe and a north–south gradient of genetic diversity. These findings identify human activities and climate as key drivers of gene flow in a wild temperate fruit tree and provide a practical basis for conservation, agroforestry, and breeding programs for apples in Europe.

Wild European apple (Malus sylvestris (L.) Mill.) population dynamics: insight from genetics and ecology in the Rhine Valley. Priorities for a future conservation programme

The increasing fragmentation of forest habitats and the omnipresence of cultivars potentially threaten the genetic integrity of the European wild apple (Malus sylvestris (L.) Mill). However, the conservation status of this species remains unclear in Europe, other than in Belgium and the Czech Republic, where it has been declared an endangered species. The population density of M. sylvestris is higher in the forests of the upper Rhine Valley (France) than in most European forests, with an unbalanced age-structure, an overrepresentation of adults and a tendency to clump. We characterize here the ecology, age-structure and genetic diversity of wild apple populations in the Rhine Valley. We use these data to highlight links to the history of this species and to propose guidelines for future conservation strategies. In total, 255 individual wild apple trees from six forest stands (five floodplain forests and one forest growing in drier conditions) were analysed in the field, collected and genotyped on the basis of data for 15 microsatellite markers. Genetic analyses showed no escaped cultivars and few hybrids with the cultivated apple. Excluding the hybrids, the genetically “pure” populations displayed high levels of genetic diversity and a weak population structure. Age-structure and ecology studies of wild apple populations identified four categories that were not randomly distributed across the forests, reflecting the history of the Rhine forest over the last century. The Rhine wild apple populations, with their ecological strategies, high genetic diversity, and weak traces of crop-to-wild gene flow associated with the history of these floodplain forests, constitute candidate populations for inclusion in future conservation programmes for European wild apple.

Independent domestications of cultivated tree peonies from different wild peony species

An understanding of plant domestication history provides insights into general mechanisms of plant adaptation and diversification and can guide breeding programmes that aim to improve cultivated species. Cultivated tree peonies (genus Paeonia L.) are among the most popular ornamental plants in the world; yet, the history of their domestication is still unresolved. Here, we explored whether the domestication in China of historically cultivated peonies, that is, the common and flare cultivated tree peonies, was a single event or whether independent domestications occurred. We used 14 nuclear microsatellite markers and a comprehensive set of 553 tree peonies collected across China, including common tree peonies, flare tree peonies and the wild species or subspecies that are potential contributors to the cultivated tree peonies, that is, Paeonia rockii ssp. rockii, P. rockii ssp. atava, P. jishanensis and P. decomposita. Assignment methods, a principal component analysis and approximate Bayesian computations provided clear evidence for independent domestications of these common tree and flare tree peonies from two distinct and allopatric wild species, P. jishanensis and P. rockii ssp. atava, respectively. This study provides the first example of independent domestications of cultivated trees from distinct species and locations. This work also yields crucial insight into the history of domestication of one of the most popular woody ornamental plants. The cultivated peonies represent an interesting case of parallel and convergent evolution. The information obtained in this study will be valuable both for improving current tree peony breeding strategies and for understanding the mechanisms of domestication, diversification and adaptation in plants.

[Surgical site infections in vaginal prolapse surgery]

INTRODUCTION

Vaginal prolapse surgery is at high risk of surgical site infections (SSI) because it's a "clean-contaminated surgery" and it's frequently associated with implantation of meshes.

OBJECTIVES

To evaluate the rate of SSI and associated risk factors in vaginal prolapse surgery with mesh support.

METHODS

In a retrospective unicenter study, two groups of patients were operated by vaginal route for a pelvic floor reconstructive surgery with mesh support. Colporraphy was made by classic surgical sutures non-coated (Monosyn(®) 3/0, B-Braun) in the first group, and surgical sutures coated with triclosan in the second group. We collected risk factors of SSIs using the procedure of the CCLIN and analyzed the occurrence of SSIs with a statistical comparative univariate analysis.

RESULTS

Study included 78 patients in the first group and 72 in the second group. SSIs total rate was 2.6 % (4 of 150), as part of 3 in the group with surgical sutures non-coated and one in the group with surgical sutures coated with triclosan (P=0.62).

CONCLUSION

In our study, SSIs rate in vaginal prolapse surgery was twice higher than classic gynecologic surgery. As the interest of using a surgical suture coated with triclosan to reduce SSI has not been demonstrated statistically, we can't recommend it.

Crop-to-wild gene flow and spatial genetic structure in the closest wild relatives of the cultivated apple

Crop‐to‐wild gene flow have important evolutionary and ecological consequences and require careful consideration in conservation programs for wild genetic resources of potential use in breeding programs and in assessments of the risk of transgene escape into natural ecosystems. Using 26 microsatellites and a set of 1181 trees, we investigated the extent of introgression from the cultivated apple, Malus domestica, to its three closest wild relatives, M. sylvestris in Europe, M. orientalis in the Caucasus, and M. sieversii in Central Asia. We found footprints of introgression from M. domestica to M. orientalis (3.2% of hybrids), M. sieversii (14.8%), and M. sylvestris (36.7%). Malus sieversii and M. orientalis presented weak, but significant genetic structures across their geographic range. Malus orientalis displayed genetic differentiation with three differentiated populations in Turkey, Armenia, and Russia. Malus sieversii consisted of a main population spread over Central Asia and a smaller population in the Tian Shan Mountains. The low Sp values suggest high dispersal capacities for the wild apple relatives. High potential for crop‐to‐wild gene flow in apples needs to be considered in the implementation of in situ and ex situ actions for the conservation of wild apple genetic resources potentially useful to plant breeding.

Evolution of pathogenicity traits in the apple scab fungal pathogen in response to the domestication of its host

Understanding how pathogens emerge is essential to bring disease-causing agents under durable human control. Here, we used cross-pathogenicity tests to investigate the changes in life-history traits of the fungal pathogen Venturia inaequalis associated with host-tracking during the domestication of apple and subsequent host-range expansion on the wild European crabapple (Malus sylvestris). Pathogenicity of 40 isolates collected in wild and domesticated ecosystems was assessed on the domesticated apple, its Central Asian main progenitor (M. sieversii) and M. sylvestris. Isolates from wild habitats in the centre of origin of the crop were not pathogenic on the domesticated apple and less aggressive than other isolates on their host of origin. Isolates from the agro-ecosystem in Central Asia infected a higher proportion of plants with higher aggressiveness, on both the domesticated host and its progenitor. Isolates from the European crabapple were still able to cause disease on other species but were less aggressive and less frequently virulent on these hosts than their endemic populations. Our results suggest that the domestication of apple was associated with the acquisition of virulence in the pathogen following host-tracking. The spread of the disease in the agro-ecosystem would also have been accompanied by an increase in overall pathogenicity.

New insight into the history of domesticated apple: secondary contribution of the European wild apple to the genome of cultivated varieties

The apple is the most common and culturally important fruit crop of temperate areas. The elucidation of its origin and domestication history is therefore of great interest. The wild Central Asian species Malus sieversii has previously been identified as the main contributor to the genome of the cultivated apple (Malus domestica), on the basis of morphological, molecular, and historical evidence. The possible contribution of other wild species present along the Silk Route running from Asia to Western Europe remains a matter of debate, particularly with respect to the contribution of the European wild apple. We used microsatellite markers and an unprecedented large sampling of five Malus species throughout Eurasia (839 accessions from China to Spain) to show that multiple species have contributed to the genetic makeup of domesticated apples. The wild European crabapple M. sylvestris, in particular, was a major secondary contributor. Bidirectional gene flow between the domesticated apple and the European crabapple resulted in the current M. domestica being genetically more closely related to this species than to its Central Asian progenitor, M. sieversii. We found no evidence of a domestication bottleneck or clonal population structure in apples, despite the use of vegetative propagation by grafting. We show that the evolution of domesticated apples occurred over a long time period and involved more than one wild species. Our results support the view that self-incompatibility, a long lifespan, and cultural practices such as selection from open-pollinated seeds have facilitated introgression from wild relatives and the maintenance of genetic variation during domestication. This combination of processes may account for the diversification of several long-lived perennial crops, yielding domestication patterns different from those observed for annual species.

Floral volatiles, pollinator sharing and diversification in the fig-wasp mutualism: insights from Ficus natalensis, and its two wasp pollinators (South Africa)

Combining biogeographic, ecological, morphological, molecular and chemical data, we document departure from strict specialization in the fig-pollinating wasp mutualism. We show that the pollinating wasps Elisabethiella stuckenbergi and Elisabethiella socotrensis form a species complex of five lineages in East and Southern Africa. Up to two morphologically distinct lineages were found to co-occur locally in the southern African region. Wasps belonging to a single lineage were frequently the main regional pollinators of several Ficus species. In South Africa, two sister lineages, E. stuckenbergi and E. socotrensis, pollinate Ficus natalensis but only E. stuckenbergi also regularly pollinates Ficus burkei. The two wasp species co-occur in individual trees of F. natalensis throughout KwaZulu-Natal. Floral volatile blends emitted by F. natalensis in KwaZulu-Natal were similar to those emitted by F. burkei and different from those produced by other African Ficus species. The fig odour similarity suggests evolutionary convergence to attract particular wasp species. The observed pattern may result from selection for pollinator sharing among Ficus species. Such a process, with one wasp species regionally pollinating several hosts, but several wasp species pollinating a given Ficus species across its geographical range could play an important role in the evolutionary dynamics of the Ficus-pollinating wasp association.

[Colpocleisis without mid-urethral sling: A valid concept in the elderly with vault vaginal prolapse and stress urinary incontinence?]

OBJECTIVES

Estimate the urinary impact of vaginal occlusion without mid-urethral sling in the elderly with vault vaginal prolapse and stress urinary incontinence.

PATIENTS AND METHODS

Retrospective case series of 22 women who underwent a vaginal closure between May 2005 and April 2009. Postoperating evaluation of the impact on the urinary tract of this surgery and of the satisfaction of the patients to a phone investigation.

RESULTS

Seventeen patients with mean age 80 years answered the phone questionnaire. With a mean follow up of 23.9 months, the rate of satisfaction amounts to 88%. The rate of recurrence is 11%. Urge incontinence decreases from 36 to 24% and there is no stress urinary incontinence postoperatively.

CONCLUSION

Colpocleisis is a surgical technique which meets high rates of satisfaction and which seems effective in the treatment of urinary incontinence associated with vaginal vault prolapse in the elderly.

A comparative immunohistochemical study of cytokeratin and vimentin expression in middle ear mucosa and cholesteatoma, and in epidermis

Cytokeratin expression was studied in human middle ear cholesteatoma lesions, using a variety of immunohistological techniques and a wide range of polyclonal antisera and monoclonal antibodies against cytokeratin (CK) subgroups or individual CK polypeptides. The expression of the other cytoskeletal proteins, vimentin and desmin, was also investigated. Middle ear mucosa and epidermal tissues were used as reference tissues. Our investigations also included epithelial structures present in the cholesteatoma perimatrix and in dermal tissues. The results indicate that, compared with epidermal tissues, the expression profile of CKs in cholesteatoma matrix is representative of a hyperproliferative disease. Evaluating the presence of a marker of terminal keratinization - the 56.5 kD acidic CK n degrees 10 - we found supportive evidence of a pronounced retardation of its expression, which did not parallel histological differentiation. In epidermal tissues, the first prickle cell layers are CK10 positive whereas in many cholesteatomas this finding was observed near the stratum granulosum only. Probing the early stages of keratinization - the 58 kD basic CK n degrees 5 and the 50 kD acidic CK n degrees 14 - we regularly observed an extended staining area in the cholesteatoma matrix. In epidermal reference tissues, only the basal and nearest suprabasal layers were convincingly labeled. As a rule, non-epidermal CKs did not belong to the cholesteatoma CK set. However, exceptions to that rule were noticed as a focal or more extended expression of one or more non-epidermal CKs in about half of the cases. Together with the extended CK5 topography, this is further evidence that CK expression is seriously affected by the diseased state. CK expression in the perimatrix is limited to mucous glands, either normal, atrophic or hyperplastic. CKs n degrees 4, 5, 7, 14, 18 and 19, also displayed by middle ear mucosa, were consistently observed. Where ductal arrangements were present, CK10 was also detected, in analogy with the CK10 registration in ductal portions of mucous glands in the external ear canal skin. The absence of CK8 in mucous glands of the perimatrix, however, strongly differentiates these structures from the mucous gland acini and ducti in the external ear canal, where CK8 is systematically expressed. Vimentin staining was restricted to dendritic cells of the matrix (Langerhans cells) and to perimatrix fibroblasts, blood cells and vascular endothelium. Coexpression of CK and vimentin was not observed.

[Technics for the study of a total leukocyte dialysate and its fractions]

The crude dialysate extracted from human white blood cells from a thousand unselected donors were studied by leukocyte migration inhibition test with measles antigen. This dialysate and its fractions eluted from Biogel P4 and P6 chromatography were compared towards rosette restoration test and nucleotide composition.